Returning an artifact you control to its owner’s hand is part of the cost of Master Transmuter’s activated ability. Paying a cost can’t be responded to (with Naturalize, for example).

2/1/2009

Since Master Transmuter is an artifact, you may return Master Transmuter itself to your hand. If you do, the rest of the ability will still work normally.

2/1/2009

The artifact card you put onto the battlefield when the ability resolves may be the same card that you returned to your hand when you paid the cost. If so, it returns to the battlefield as a new object with no relation to its previous existence.